rbbt-GE 1.0.0 → 1.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +15 -0
- data/LICENSE +1 -1
- data/lib/rbbt/GE.rb +8 -2
- data/lib/rbbt/GE/GEO.rb +1 -0
- data/share/lib/R/MA.R +30 -2
- metadata +7 -11
checksums.yaml
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data/LICENSE
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data/lib/rbbt/GE.rb
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@@ -5,8 +5,8 @@ module GE
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MA = File.join(LIB_DIR, 'MA.R')
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def self.run_R(command)
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cmd = "
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R.run(cmd)
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cmd = "\nsource('#{MA}');\n" << command
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R.run(cmd, :monitor => true)
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end
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def self.r_format(list, options = {})
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FileUtils.mkdir_p File.dirname(outfile) unless outfile.nil? or File.exists? File.dirname(outfile)
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GE.run_R("rbbt.GE.process(#{ r_format datafile }, main = #{r_format(main, :strings => true)}, contrast = #{r_format(contrast, :strings => true)}, log2=#{ r_format log2 }, outfile = #{r_format outfile}, key.field = #{r_format key_field}, two.channel = #{r_format two_channel})")
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end
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def self.barcode(datafile, outfile, factor = 2)
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FileUtils.mkdir_p File.dirname(outfile) unless outfile.nil? or File.exists? File.dirname(outfile)
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GE.run_R("rbbt.GE.barcode(#{ r_format datafile }, #{ r_format outfile }, #{ r_format factor })")
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end
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end
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data/lib/rbbt/GE/GEO.rb
CHANGED
data/share/lib/R/MA.R
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@@ -1,5 +1,35 @@
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library(limma)
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#########################################################################
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# BARCODE
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rbbt.GE.barcode <- function(matrix_file, output_file, sd.factor = 2){
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data = rbbt.tsv(matrix_file)
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data.mean = rowMeans(data, na.rm=T)
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data.sd = apply(data, 1, sd, na.rm=T)
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data.threshold = as.matrix(data.mean) + sd.factor * as.matrix(data.sd)
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names(data.threshold) = names(data.mean)
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rm(data.mean)
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rm(data.sd)
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file.barcode = file(output_file, 'w')
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cat("#Ensembl Gene ID", file = file.barcode)
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cat("\t", file = file.barcode)
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cat(colnames(data), file = file.barcode, sep="\t")
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cat("\n", file = file.barcode)
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for (gene in rownames(data)){
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barcode = (data[gene,] - data.threshold[gene]) > 0
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cat(gene, file = file.barcode)
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cat("\t", file = file.barcode)
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cat(barcode, file = file.barcode, sep = "\t")
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cat("\n", file = file.barcode)
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}
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close(file.barcode)
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}
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#########################################################################
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# Model processing
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@@ -529,6 +559,4 @@ MA.load <- function(prefix, orders = TRUE, logratios = TRUE, t = TRUE, p.values
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return(data);
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-
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-
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}
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metadata
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--- !ruby/object:Gem::Specification
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name: rbbt-GE
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version: !ruby/object:Gem::Version
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version: 1.
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prerelease:
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version: 1.1.0
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platform: ruby
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authors:
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- Miguel Vazquez
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autorequire:
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bindir: bin
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cert_chain: []
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date:
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date: 2013-10-21 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rbbt-util
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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@@ -39,32 +36,31 @@ files:
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- lib/rbbt/GE/GEO.rb
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- share/install/GEO/Rakefile
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- share/lib/R/MA.R
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- test/test_helper.rb
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- test/rbbt/GE/test_GEO.rb
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- test/test_helper.rb
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homepage: http://github.com/mikisvaz/rbbt-GE
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licenses: []
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metadata: {}
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post_install_message:
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rdoc_options: []
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require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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required_rubygems_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version:
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rubygems_version: 2.0.3
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signing_key:
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specification_version:
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specification_version: 4
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summary: Gene Expression in RBBT
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test_files:
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- test/test_helper.rb
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- test/rbbt/GE/test_GEO.rb
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- test/test_helper.rb
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